Aircraft: B747
Phase of flight: Initial Climb
Anomaly: Aircraft Equipment Problem Critical

Upon completion of flap retraction; felt mild thump followed by onset of continuous low frequency buzz and mild vibration in area of door 2R. As relief captain; I visually inspected wing leading edges and upper wing area from cabin windows on both sides of aircraft. Found nothing irregular. Also noticed a mild squeal emanating from upper area of door 2R seal. All handling; system operation and flight characteristics normal with no pressurization issues throughout all phases of flight. Consulted with Dispatch and Maintenance Control. Discussion concluded possible door seal pinched / exposed to slip stream or conditioned air belly door ajar. Decided to continue while monitoring status. As flight entered ZZZ airspace [five plus hours into flight]; reevaluated vibration and decided it was getting bad enough to land and investigate after consulting again with Dispatch and Maintenance. Declared emergency and diverted to ZZZ. Subsequent descent; approach and landing normal. Initially dumped 25k lbs of fuel (30k feet) then another 10k lbs (6k+ feet) closer to initial approach. Max landing weight upon touchdown. Weather on landing: calm winds; 4 nm visibility; 1600 ft overcast; light snow. Reported BRAC good - fair with runway swept and sprayed for our arrival. Emergency equipment was requested and they were out upon landing but not needed or used. Braking action for us was good. Briefed Cat III approach & autoland which was executed with no problems. Subsequent descent; approach and landing normal. Upon arrival at gate; were met at airplane by FAA (local; district and region); NTSB (local and region); Company service manager; Pegasus maintenance and local police. Passengers were handled quickly by service manager. Cabin crew was transported to hotel. Pilots remained at aircraft until FAA & NTSB assured of power removed from FDR and DVR. Gave brief facts verbally to FAA and NTSB. Inspection by maintenance and pilots revealed two ACM [Air Cycle Machine] belly panels departed airplane. Also noted multiple holes in belly next to & aft of departed panels. Noted a partial puncture hole on case of forward-most right ACM. No other damage observed. If maintenance was done in this area; verify integrity of ACM belly panel security before release for flight. If no maintenance was done; perhaps schedule periodic inspections of ACM belly panel attachments on a more frequent basis than presently done. Five plus hours after takeoff; Purser noticed an increase in intensity of noise and vibration. Two relief pilot crew inspected and concurred with that assessment. I went to that area personally and noticed vibration and loud noise from the floor area rows 21-38; 2R to 3R.Flight crew consensus determined possible structural failure and immediate divert to a suitable airport. Conferred with Dispatch and Maintenance and determined ZZZ weather was now suitable for landing under the conditions as opposed to ZZZ1. B747 flight crew experienced a mild thump followed by onset of continuous low frequency buzz and mild vibration in the area of Door 2R; upon completion of flap retraction. No faults can be found and the flight continues for several hours before the crew elects to divert for maintenance inspection. Two ACM (pack) panels are found missing from the belly of the aircraft.